| 1. |
- Achilles, Silvio, et al.
(författare)
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GPU-Accelerated Coupled Ptychographic Tomography
- 2022
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Ingår i: Developments in X-Ray Tomography XIV. - : SPIE. - 0277-786X .- 1996-756X. - 9781510654686 ; 12242
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Konferensbidrag (refereegranskat)abstract
- Scanning coherent X-ray microscopy (ptychography) has gained considerable interest during the last decade since the performance of this indirect imaging technique does not necessarily rely on the quality of the X-ray optics and, in principle, can achieve highest spatial resolution in X-ray imaging. The method can be easily extended to 3D by adding standard tomographic reconstruction schemes. However, the tomographic reconstruction is often applied in a subsequent step using a sequence of aligned ptychographic 2D projections. In this contribution, we outline current developments of a GPU-accelerated framework for direct 3D ptychography, coupling 2D ptychography and tomography. The program utilizes a custom GPU-accelerated framework for ptychography that offers three distinct ptychographic reconstruction algorithms. The tomographic reconstruction runs simultaneously and uses numerical routines of the ASTRA Toolbox. This parallel-computing approach results in a high performance increase considerably reducing the reconstruction time of 3D ptychographic datasets.
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| 2. |
- Bauwens, Maite, et al.
(författare)
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Recent past (1979-2014) and future (2070-2099) isoprene fluxes over Europe simulated with the MEGAN-MOHYCAN model
- 2018
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 15:12, s. 3673-3690
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Tidskriftsartikel (refereegranskat)abstract
- Isoprene is a highly reactive volatile organic compound emitted by vegetation, known to be a precursor of secondary organic aerosols and to enhance tropospheric ozone formation under polluted conditions. Isoprene emissions respond strongly to changes in meteorological parameters such as temperature and solar radiation. In addition, the increasing CO2 concentration has a dual effect, as it causes both a direct emission inhibition as well as an increase in biomass through fertilization. In this study we used the MEGAN (Model of Emissions of Gases and Aerosols from Nature) emission model coupled with the MOHYCAN (Model of HYdrocarbon emissions by the CANopy) canopy model to calculate the isoprene fluxes emitted by vegetation in the recent past (1979-2014) and in the future (2070-2099) over Europe at a resolution of 0.1° × 0.1°. As a result of the changing climate, modeled isoprene fluxes increased by 1.1%yr-1 on average in Europe over 1979-2014, with the strongest trends found over eastern Europe and European Russia, whereas accounting for the CO2 inhibition effect led to reduced emission trends (0.76%yr-1). Comparisons with field campaign measurements at seven European sites suggest that the MEGAN-MOHYCAN model provides a reliable representation of the temporal variability of the isoprene fluxes over timescales between 1h and several months. For the 1979-2014 period the model was driven by the ECMWF ERA-Interim reanalysis fields, whereas for the comparison of current with projected future emissions, we used meteorology simulated with the ALARO regional climate model. Depending on the representative concentration pathway (RCP) scenarios for greenhouse gas concentration trajectories driving the climate projections, isoprene emissions were found to increase by +7% (RCP2.6), +33% (RCP4.5), and +83% (RCP8.5), compared to the control simulation, and even stronger increases were found when considering the potential impact of CO2 fertilization: +15% (RCP2.6), +52% (RCP4.5), and +141% (RCP8.5). However, the inhibitory CO2 effect goes a long way towards canceling these increases. Based on two distinct parameterizations, representing strong or moderate inhibition, the projected emissions accounting for all effects were estimated to be 0-17% (strong inhibition) and 11-65% (moderate inhibition) higher than in the control simulation. The difference obtained using the two CO2 parameterizations underscores the large uncertainty associated to this effect.
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| 3. |
- Bech, Martin, et al.
(författare)
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Dual-binary phase gratings for x-ray interferometry
- 2022
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Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 9781510654686
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Konferensbidrag (refereegranskat)abstract
- X-ray phase-contrast imaging by grating interferometry has in the past decades been established both at synchrotron radiation sources and at conventional x-ray tubes. Due to the sensitivity to x-ray phase shifting, contrast in soft tissue has been improved significantly and the possibilities to do virtual histology of tissue biopsies are being pioneered. Constraints in the design of a grating interferometer are dominated by the phase-shifting structures of the gratings. Typically, binary gratings are used, with alternating regions of shift and no shift. However, other structures are also possible, leading to different patterns of intensity modulations. Here we simulate the possibility of using multiple binary structures in the phase grating, to utilize Moiré effects and avoid the use of attenuating grating structures. In particular the parameters for grating-based phase-contrast imaging using a single optical element are discussed, with focus on laboratory-based x-ray imaging using microfocus sources.
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| 4. |
- Bergamaschi, Peter, et al.
(författare)
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High-resolution inverse modelling of European CH4emissions using the novel FLEXPART-COSMO TM5 4DVAR inverse modelling system
- 2022
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 22:20, s. 13243-13268
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Tidskriftsartikel (refereegranskat)abstract
- We present a novel high-resolution inverse modelling system ("FLEXVAR") based on FLEXPARTCOSMO back trajectories driven by COSMO meteorological fields at 7 km×7 km resolution over the European COSMO-7 domain and the four-dimensional variational (4DVAR) data assimilation technique. FLEXVAR is coupled offline with the global inverse modelling system TM5-4DVAR to provide background mole fractions ("baselines") consistent with the global observations assimilated in TM5-4DVAR. We have applied the FLEXVAR system for the inverse modelling of European CH4 emissions in 2018 using 24 stations with in situ measurements, complemented with data from five stations with discrete air sampling (and additional stations outside the European COSMO-7 domain used for the global TM5-4DVAR inversions). The sensitivity of the FLEXVAR inversions to different approaches to calculate the baselines, different parameterizations of the model representation error, different settings of the prior error covariance parameters, different prior inventories, and different observation data sets are investigated in detail. Furthermore, the FLEXVAR inversions are compared to inversions with the FLEXPART extended Kalman filter ("FLExKF") system and with TM5-4DVAR inversions at 1° × 1° resolution over Europe. The three inverse modelling systems show overall good consistency of the major spatial patterns of the derived inversion increments and in general only relatively small differences in the derived annual total emissions of larger country regions. At the same time, the FLEXVAR inversions at 7 km × 7 km resolution allow the observations to be better reproduced than the TM5-4DVAR simulations at 1° × 1°. The three inverse models derive higher annual total CH4 emissions in 2018 for Germany, France, and BENELUX compared to the sum of anthropogenic emissions reported to UNFCCC and natural emissions estimated from the Global Carbon Project CH4 inventory, but the uncertainty ranges of top-down and bottom-up total emission estimates overlap for all three country regions. In contrast, the top-down estimates for the sum of emissions from the UK and Ireland agree relatively well with the total of anthropogenic and natural bottom-up inventories.
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| 5. |
- Bert, Valérie, et al.
(författare)
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How to manage plant biomass originated from phytotechnologies? : Gathering perceptions from end-users
- 2017
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Ingår i: International journal of phytoremediation. - : Taylor & Francis. - 1522-6514 .- 1549-7879. ; 19:10, s. 947-954
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Tidskriftsartikel (refereegranskat)abstract
- A questionnaire survey was carried out in 4 European countries to gather end-user's perceptions of using plants from phytotechnologies in combustion and anaerobic digestion (AD). 9 actors of the wood energy sector from France, Germany and Sweden, and 11 AD platform operators from France, Germany and Austria were interviewed. Questions related to installation, input materials, performed analyses, phytostabilization and phytoextraction. Although the majority of respondents did not know phytotechnologies, results suggested that plant biomass from phytomanaged areas could be used in AD and combustion, under certain conditions. As a potential advantage, these plants would not compete with plants grown on agricultural lands, contaminated lands being not suitable for agriculture production. Main limitations would be related to additional controls in process' inputs and end-products and installations that might generate additional costs. In most cases, price of phytotechnologies biomass was mentioned as a driver to potentially use plants from metal-contaminated soils. Plants used in phytostabilisation or phytoexclusion were thought to be less risky and, consequently, benefited from a better theoretical acceptance than those issued from phytoextraction. Results were discussed according to national regulations. One issue related to the regulatory gap concerning the status of the plant biomass produced on contaminated land.
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| 6. |
- Dreier, Till, et al.
(författare)
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Radiopaque dyes allow vessel imaging in lung tissue using laboratory phase contrast micro-CT
- 2022
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Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. ; 12242
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Konferensbidrag (refereegranskat)abstract
- Phase contrast micro-CT is a powerful technique allowing imaging of soft tissue at synchrotrons or using lab- oratory sources. The use of contrast agents is a useful approach when imaging vascular structures. However, common x-ray contrast agents typically rely on heavy metals to increase absorption, which may affect the phase contrast and cause artifacts in the reconstructed volumes. Thus, utilizing an agent with lower attenuation similar to soft tissue is clearly advantageous. Here, we evaluated different colored radiopaque solutions (tissue marking dyes) which had been injected into the vascular system of bovine lung samples, prior to embedding in paraffin. Scans were performed using a micro-focus x-tube calibrated to 10 µm spot size at 70 kV and a photon counting detector with a silicon sensor and 75 µm pixels. The resulting volumes have a voxel size of (25 µm)3, limited by the size of the samples, but sufficient to resolve the vascular system. Experiments confirmed that sufficient perfusion of the vessels with the dyes could be achieved, and the different dyes could be clearly discerned in the reconstructed volumes without causing artifacts allowing to clearly identify features in the soft tissue. Further, the findings were confirmed by histology.Keywords:
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| 7. |
- Kumpiene, Jurate, et al.
(författare)
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Selecting chemical and ecotoxicological test batteries for risk assessment of trace element-contaminated soils (phyto)managed by gentle remediation options (GRO)
- 2014
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 496, s. 510-522
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Tidskriftsartikel (refereegranskat)abstract
- During the past decades a number of field trials with gentle remediation options (GRO) have been established on trace element (TE) contaminated sites throughout Europe. Each research group selects different methods to assess the remediation success making it difficult to compare efficacy between various sites and treatments. This study aimed at selecting a minimum risk assessment battery combining chemical and ecotoxicological assays for assessing and comparing the effectiveness of GRO implemented in seven European case studies. Two test batteries were pre-selected; a chemical one for quantifying TE exposure in untreated soils and GRO-managed soils and a biological one for characterizing soil functionality and ecotoxicity. Soil samples from field studies representing one of the main GROs (phytoextraction in Belgium, Sweden, Germany and Switzerland, aided phytoextraction in France, and aided phytostabilization or in situ stabilization/phytoexclusion in Poland, France and Austria) were collected and assessed using the selected test batteries. The best correlations were obtained between NH4NO3-extractable, followed by NaNO3-extractable TE and the ecotoxicological responses. Biometrical parameters and biomarkers of dwarf beans were the most responsive indicators for the soil treatments and changes in soil TE exposures. Plant growth was inhibited at the higher extractable TE concentrations, while plant stress enzyme activities increased with the higher TE extractability. Based on these results, a minimum risk assessment battery to compare/biomonitor the sites phytomanaged by GROs might consist of the NH4NO3 extraction and the bean Plantox test including the stress enzyme activities.
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| 8. |
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| 9. |
- Mollenhauer, Jan, et al.
(författare)
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Carcinogen inducibility in vivo and down-regulation of DMBT1 during breast carcinogenesis.
- 2004
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Ingår i: Genes, chromosomes & cancer. - : Wiley. - 1045-2257. ; 39:3, s. 185-94
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Tidskriftsartikel (refereegranskat)abstract
- Deleted in malignant brain tumors 1 (DMBT1) has been proposed as a candidate tumor suppressor for brain and epithelial cancer. Initial studies suggested loss of expression rather than mutation as the predominant mode of DMBT1 inactivation. However, in situ studies in lung cancer demonstrated highly sophisticated changes of DMBT1 expression and localization, pointing to a chronological order of events. Here we report on the investigation of DMBT1 in breast cancer in order to test whether these principles might also be attributable to other tumor types. Comprehensive mutational analyses did not uncover unambiguous inactivating DMBT1 mutations in breast cancer. Expression analyses in the human and mouse mammary glands pointed to the necessity of DMBT1 induction. While age-dependent and hormonal effects could be ruled out, 9 of 10 mice showed induction of Dmbt1 expression after administration of the carcinogen 7,12-dimethybenz(alpha)anthracene prior to the onset of tumorigenesis or other histopathological changes. DMBT1 displayed significant up-regulation in human tumor-flanking tissues compared to in normal breast tissues (P < 0.05). However, the breast tumor cells displayed a switch from lumenal secretion to secretion to the extracellular matrix and a significant down-regulation compared to that in matched normal flanking tissues (P < 0.01). We concluded that loss of expression also is the predominant mode of DMBT1 inactivation in breast cancer. The dynamic behavior of DMBT1 in lung carcinoma is fully reflected in breast cancer, which suggests that this behavior might be common to tumor types arising from monolayered epithelia.
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| 10. |
- Moosmann, Julian, et al.
(författare)
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A load frame for in situ tomography at PETRA III
- 2019
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Ingår i: Developments in X-Ray Tomography XII. - : SPIE. - 0277-786X .- 1996-756X. - 9781510629196 ; 11113
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- A load frame for in situ mechanical testing is developed for the microtomography end stations at the imaging beamline P05 and the high-energy material science beamline P07 of PETRA III at DESY, both operated by the Helmholtz- Zentrum Geesthacht. The load frame is fully integrated into the beamline control system and can be controlled via a feedback loop. All relevant parameters (load, displacement, temperature, etc.) are continuously logged. It can be operated in compression or tensile mode applying forces of up to 1 kN and is compatible with all contrast modalities available at IBL and HEMS i.e. conventional attenuation contrast, propagation based phase contrast and differential phase contrast using a grating interferometer. The modularity and flexibility of the load frame allows conducting a wide range of experiments. E.g. compression tests to understand the failure mechanisms in biodegradable implants in rat bone or to investigate the mechanics and kinematics of the tessellated cartilage skeleton of sharks and rays, or tensile tests to illuminate the structure-property relationship in poplar tension wood or to visualize the 3D deformation of the tendonbone insertion. We present recent results from the experiments described including machine-learning driven volume segmentation and digital volume correlation of load tomography sequences.
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